The detection of pathogenic microorganisms in biological fluids should be performed in the shortest possible time, in particular in the case of septicemia for which the mortality remains high in spite of the broad range of antibiotics which are available to doctors. The presence of biologically active agents such as a microorganism in a patient's body fluid, especially blood, is generally determined using blood culture bottles. Bloodstream infections are associated with high morbidity and mortality, yet current diagnostic methods, of culture followed by biochemical identification and antibiotic susceptibility testing, can take several days to perform. Typically, empiric therapy is initiated based on clinical symptoms, and test results only impact clinical decisions when the initial therapy fails. The ability to characterize bloodstream infections within the first few hours, preferably within an hour after a positive blood culture result would significantly boost the clinical relevance of the diagnostic information provided. Molecular amplification methods have been proposed to fill this need, but serious challenges to this approach remain. The positive blood culture broth itself represents a naturally amplified population of microorganisms with potential for use in a variety of rapid, identification (ID) tests.
Traditional automated phenotypic ID tests, such as the VITEK®, PHOENIX®, and MICROSCAN® systems, or manual phenotypic tests such as API require that microorganisms be in an appropriate growth phase and free of interfering media and blood products in order to provide robust results. These systems use colonies grown from the positive broth for 18-24 hours on plated media. However, in an effort to obtain faster results, some laboratories have reported using these systems with microorganisms isolated from positive blood culture bottles. These direct-from-the-bottle tests are not appropriate for all microorganisms (e.g., Gram-positive cocci), are not validated by the test manufacturers, and generally take 3-8 hours to provide results. Faster and more broadly specific tests are urgently needed in order to provide the physician with clinically relevant results within the first few hours, preferably within an hour after a positive culture result.
Mass spectrometric methods have the potential to allow for identification of microorganisms very quickly, but may encounter interference from the many compounds present in liquid microbiological culture media and in clinical samples such as blood or combinations thereof. The most commonly employed methods for recovering microorganisms directly from positive blood culture broth are two-step differential centrifugation and centrifugation in a serum separator tube.
Other methods for separation, characterization and/or identification of microorganisms have been described, include:
In U.S. Pat. No. 7,070,739 a method is presented to extract, separate, and purify microbes including viruses by two-dimensional ultra-centrifuging directly from body fluids or homogenized tissue. In a first centrifuging step, all particles are removed having a sedimentation speed higher than those of the microbes to be identified. In the second ultra-centrifuging step, isopycnic banding is used in liquids filled in to form a wide-range density gradient, using special serrated centrifuge tubes. According to the patent, the separation technique can be used for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes.
EP0533912A describes a sample pretreatment apparatus and method for dialysis fluid and urine. The patent application describes the use of a large pore size pre-filter to remove typical urinary sediments such as blood cells, epithelial cells, casts, mucus and crystals. Any bacteria present pass through the pre-filter and are captured on a second downstream filter. Captured bacteria are then accessed by manually disassembling the stacked apparatus.
U.S. Pat. Appl. Pub. No. 2007/0175278 describes using a liquid culture medium for culturing a sample of interest, including for example, blood, urine, feces, intravenous catheters etc., industrial production lines, water systems, a food product, a cosmetic product, a pharmaceutical product and a forensic sample. Subsequently, the microorganisms can be harvested from the liquid medium by methods known in the art, e.g. by centrifugation. The concentrated microorganisms may then be transferred to carrier material, optionally after drying, for obtaining a vibrational spectrum. The patent application discusses various methods for identifying and classifying microorganisms, including vibrational spectroscopy, such as Raman spectroscopy.
However, these methods have several drawbacks when attempting to separate and characterize microorganisms from some clinical test samples (e.g., complex samples such as blood-containing culture media). In the case of blood-containing culture media, the resultant microbial preparations often contain contaminating red blood cells, platelets, lipid particles, plasma enzymes and cellular debris, which can cause poor results. These methods are also very labor-intensive and unsafe due to steps which can result in aerosol exposure of potentially dangerous pathogens to the user.
Co-assigned U.S. Pat. Appl. Pub. No. 2010/0120085, which is incorporated herein, describes methods for separating, characterizing and/or identifying microorganisms in a test sample. The method described a sample preparation procedure comprising of a selective lysis step and subsequent separation step for the isolation and purification of an unknown microorganism from a test sample for identification of the microorganism using mass spectrometry. The application also describes using filtration for the isolation and purification of an unknown microorganism from a test sample.
Nevertheless, there remains a need for improved sample preparation methods and kits for the isolation, accumulation and/or purification of microorganisms from clinical test samples, which are compatible with rapid identification technologies such as mass spectrometry. The methods and devices described herein produce a clean, concentrated, sample of microorganisms that is optimal for analysis, for example, by mass spectrometry, especially for MALDI-TOF MS analysis.